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- PDB-7p18: Crystal structure of 3-ketosteroid delta1-dehydrogenase from Ster... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p18 | ||||||
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Title | Crystal structure of 3-ketosteroid delta1-dehydrogenase from Sterolibacterium denitrificans in complex with 1,4-androstadiene-3,17-dione | ||||||
![]() | 3-oxosteroid 1-dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Flavoprotein / Dehydrogenase / 3-Ketosteroid Delta1-dehydrogenase / 3-Ketosteroid Dehydrogenase / 3-Oxosteroid Dehydrogenase / Rossmann Fold | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wojcik, P. / Mrugala, B. / Kurpiewska, K. / Szaleniec, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure, Mutagenesis, and QM:MM Modeling of 3-Ketosteroid Delta 1 -Dehydrogenase from Sterolibacterium denitrificans ─The Role of a New Putative Membrane-Associated Domain and Proton- ...Title: Structure, Mutagenesis, and QM:MM Modeling of 3-Ketosteroid Delta 1 -Dehydrogenase from Sterolibacterium denitrificans ─The Role of a New Putative Membrane-Associated Domain and Proton-Relay System in Catalysis. Authors: Wojcik, P. / Glanowski, M. / Mrugala, B. / Procner, M. / Zastawny, O. / Flejszar, M. / Kurpiewska, K. / Niedzialkowska, E. / Minor, W. / Oszajca, M. / Bojarski, A.J. / Wojtkiewicz, A.M. / Szaleniec, M. #1: Journal: Int J Mol Sci / Year: 2022 Title: 1,2-Hydrogenation and Transhydrogenation Catalyzed by 3-Ketosteroid Delta 1 -Dehydrogenase from Sterolibacterium denitrificans -Kinetics, Isotope Labelling and QM:MM Modelling Studies. Authors: Wojtkiewicz, A.M. / Glanowski, M. / Waligorski, P. / Janeczko, T. / Szaleniec, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 250.7 KB | Display | ![]() |
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PDB format | ![]() | 197.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 49.1 KB | Display | |
Data in CIF | ![]() | 72.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c3yS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 5 - 560 / Label seq-ID: 5 - 560
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61427.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: acmB, SDENCHOL_10486 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 838 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/ANB.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ANB.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ANB / | #4: Chemical | ChemComp-PEG / #5: Chemical | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.48 % / Description: bright yellow rhombohedral crystal |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 293 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2021 |
Radiation | Monochromator: DCM Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→47.71 Å / Num. obs: 119085 / % possible obs: 99.52 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.4 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.057 / Rrim(I) all: 0.07 / Rsym value: 0.129 / Net I/av σ(I): 1.6 / Net I/σ(I): 1.6 |
Reflection shell | Resolution: 1.84→1.89 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.719 / Num. unique obs: 5860 / CC1/2: 0.515 / Rpim(I) all: 0.753 / Rrim(I) all: 0.486 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4C3Y Resolution: 1.84→47.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.25 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.846 Å2
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Refinement step | Cycle: 1 / Resolution: 1.84→47.71 Å
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Refine LS restraints |
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